The Bottleship Incident
by Savato93
Summary: Following the events of Super Metroid and the destruction of Zebes, Samus Aran is called upon to escort a team of Federation Marines into hostile territory in the search for lost precious cargo; what they find instead will shake the Federation to its very core. A PROPER telling of Metroid: Other M, rated M for safety.
1. Once More, Unto the Breach

Disclaimer: Metroid is the property of Nintendo. I OWN NOTHING!

* * *

_Her life had flashed before her eyes, and there wasn't much good in it._

_Sure, she had rid the galaxy of Dark Samus and Phazon. Sure, she had single-handedly reduced the Metroid race to a single hatchling. Sure, she had enacted justice against the monster that murdered her parents… several times over._

_But Samus Aran had failed in the one task that mattered most to her: she allowed Mother Brain to survive. And now, as she glared up at the abomination that ruled over the Space Pirate race, she silently chastised herself, running countless simulations of what might have been, had she taken a different action in their first confrontation._

_She could have called in the Federation for cleanup; lock down the star system, allow nothing a chance to escape or rebuild. She could have detonated a planet-breaker and outright annihilated Zebes, galactic code be damned. And most importantly… she could have checked the fucking _corpse…

_And now, here she was. Through the rigid alloys that made up her breastplate, she could feel multiple fractured ribs, at least one broken and puncturing her lungs. A single mistimed leap, and a concussive blast had thrown her into the wall, bending her right leg beyond the limits of even her limber form. And all the internal bleeding and organ trauma…_

_Samus tried to raise her cannon, twist into her morph ball, _something_… she was certain she could persevere, but her suit had reached its limits. Whatever that beam was that Mother Brain fired, it had detonated her vast explosive arsenal inside of her suit in a cataclysmic chain reaction. What little energy her damaged reactor was producing, it was being devoted to keeping her life support functioning._

_She'd never expected her life to end like this—broken and bleeding, prostrate before the abomination she'd spent so long tracking down, and who could now snuff out her light effortlessly. Personally, she'd expected to end her life on the receiving end of the bullet of an unseen assassin, firing from fifteen miles away with a sub-light sniper rifle. If things didn't come to that, passing away by old age was a close second… but with all her genetic modifications, the odds of that happening were slim to none, so it was kind of a no-win situation._

"YOU WERE GIVEN AN OPPORTUNITY, ONCE UPON A TIME."_ Mother Brain's booming voice reverberated through Samus's skull. _"I AM NOT UNWILLING TO SPARE YOU, TO GIVE YOU A SECOND CHANCE, DESPITE WHAT YOU HAVE DONE ON THIS WORLD. JOIN ME, AND WE SHALL RULE THIS PITIFUL REALM OF EXISTENCE, SIDE BY SIDE."

_Samus's only response was to raise her left hand, middle finger extended in a blatant gesture of defiance._

_Mother Brain hissed. _"SO BE IT. LET HISTORY KNOW THAT I GAVE YOU A CHOICE."

_As the monster's single eye began to glow a brilliant crimson, Samus polarized her visor and braced herself for the end…_

* * *

The thing that brought Samus back into the world of the living was the pain. Funny thing, that. Pain was… well, pain, but she welcomed it because it let her know she was still alive. When she _didn't _feel pain, there was no telling what might happen to her.

She turned her thoughts from pain to the conscious world, and found herself staring up into the plain white light of a Federation medical ward. How…?

Then the memories came flooding back. The Metroid hatchling, the last of its kind, had attacked Mother Brain at the last second, crippling her with her own energy and saving Samus's life. At the cost of its own life, the Metroid gave Samus the strength she needed to finish the job, destroying Mother Brain once and for all. Then, she'd limped all the way back to her ship, remaining conscious long enough to set a course to a Federation outpost before blacking out.

It was funny, Samus thought. In typical fairy-tales a baby wakes up, and identifies the first organism in its sights as its mother. And yet, the Metroid attached itself to her the moment it broke free of its egg. At first, she assumed it was merely confused, unsure of its own instincts—something she was all too quick to confirm when it attacked her in Tourian, having grown to nearly half the size of her gunship. But then, it _stopped_… detached itself from her body and chirped in a… _happy_ tone. And then, not hours later, it saved her life. It just didn't seem natural, and yet…

"Welcome to the G.F.S. _Montana_, Samus Aran." A calm, synthetic voice greeted Samus. "Your armor is currently undergoing repair in the armory. It should be ready for you within the next 30 minutes. Your new undersuit will be brought to you shortly."

Excellent; just enough time for some meditation. Samus sat up, ignoring the protests of her battered body, and plucked the intravenous drip from her arm. About this time, that last part of the AI's statement sank in—she was wearing naught but a hospital gown. With a '…meh' reaction, Samus took a seat on the cold floor and began to recite the lines of a simple Chozo hymn.

She was too absorbed in her meditation to notice when a door on the far side of the room opened up. "I was just notified by the… ah." The woman who entered the room got a full view of Samus's highly-toned back and shoulder muscles. "Samus Aran?" Samus stood up and turned to face the newcomer.

Samus examined the woman's ID. _Francine Maliki, Xenobiologist_. Samus had the feeling that the universe was playing some sort of cruel trick on her; for all her alterations, she was still _human_. She nodded.

"Anyway, here is your undersuit." The doctor handed Samus her Zero Suit module. "I don't mean to be intrusive, but I've been hearing some rumors about what happened down on Zebes. Is it true that your life was saved by a Metroid that mistook you for its mother?"

Samus remained silent, but nodded again. The doctor continued. "I may not have anything to do with it, but for what it's worth, I'm sorry you had to go through that sort of loss." When she received no answer right away, the doctor guessed she wasn't getting one and moved to leave.

Just as the doctor turned away, Samus spoke. "Death is just a part of life. I'd be a fool to cling to any one instance."

The doctor glanced back. "I see. Well, I'll leave you to your… whatever it is you're doing." She quietly departed.

Samus sighed. It was so hard for her to interact with the common people, for whatever reason. Not that it particularly mattered to her, being the solitary sort, but sometimes she just wanted to have the comfort of somebody willing to stand with her.

She silently attached the module to the base of her neck. With a thought, her hospital gown fell apart, and the Zero Suit enveloped her form. Samus began to relax as the suit molded to her body shape, becoming like a second skin once more.

"_Samus Aran, a high-ranking Federation official wishes to speak to you."_ The AI spoke up. _"He is waiting on channel 597-B."_

Samus sighed. So much for meditation.

* * *

"_Samus."_ The gruff, but calm voice of Fleet Admiral Castor Dane greeted her. He hadn't changed much appearance-wise from the last time Samus has seen him, though there were some new wrinkles on his brow and in the corners of his eyes. _"Are you pulling yourself together well enough?"_

"Nothing I won't recover from, Admiral." Samus stood straight, hands clasped behind her back as she faced the hologram. "How have you been doing?"

Dane removed his cap and ran a hand over his greying, buzz-cut hair. _"I won't lie; the past year has been somewhat straining. Dark Samus and Phazon carried a hell of a lot of influence; when you destroyed Phaaze, you also brought down close to 90% of the Space Pirates' standing fleet. With their numbers so severely reduced, it's actually becoming harder to track down their movements. It's a shame that Zebes was rigged to blow."_

"That's probably the reaction Mother Brain was going for," Samus replied, shrugging. "If she fell, she made sure nobody would be able to recover any data."

"_I suppose it was a masterpiece of the Chozo for a reason. Always having a plan for every possible outcome."_ Dane nodded solemnly, silently taking note of Samus's referring to Mother Brain as a 'she.' _"It's for the best that you brought Mother Brain down for good."_

"How true." Samus nodded in turn. When she looked back up, her eyebrows were raised. "But, I suppose you weren't calling just to check up on me?"

A smirk tugged at the corner of the Admiral's lips. _"No. I have an assignment I'd like you to undertake."_

_Out of the frying pan, straight into another frying pan. Just another day in the life of Samus Aran._ "Details?"

"_Straight to the point, as always. Nice to see Mother Brain didn't have an effect on your sense of duty."_ Dane replaced his cap. _"While you were recovering, Federation scientists scrubbed what was left of your suit for organic residue. They were hoping to find enough intact DNA to permit cloning of native Zebesian organisms rendered extinct by the destruction of the planet."_

With a frown, Samus brought her arms out from behind her back, folding them in front of her. "And the Metroid."

Dane sighed and nodded. _"Yes, the Metroid, too. We wanted to pick up where the unfortunate souls at Ceres Station left off, researching the Metroid's energy-generating potential for the good of galactic civilization."_

_Ah, yes, Ceres Station. Where this entire mess with the Metroid hatchling started. I'm still amazed that the Space Pirates got all the way to Sol without being detected._ "So, just how far did the scientists get before shit hit the fan?" Samus asked.

Dane chuckled. It was a rare occurrence for Samus Aran to swear. _"Pretty far, actually. They managed to get the DNA samples off the _Montana_ without being attacked. Three hours after they left, though, we lost contact with them. So far, the Federation is assuming this is the work of pirates."_

Well, it was certainly better than the last time. She'd barely had five minutes between delivering the hatchling to Ceres, and the station coming under attack by Ridley. "Space Pirates?"

"_No. Typical galactic delinquents, sacking cargo ships for a living. Search parties were quick to arrive on the scene, considering the nature of this cargo. The ship itself was missing, but we were able to determine the pirates' escape vector."_

"Well, that's good news, for a change. Where does the trail lead?"

"_The subspace ripples terminate on the outskirts of the Epsilon Indi system. That entire galactic sector is a hotbed of anti-Federation activity, hence the Federation's assumption of pirates. Luckily, the Federation is running a deep-cover operation in that same system, so we can coordinate our efforts with agents present._

"_This is where you come in. the Federation has the 07__th__ Platoon on standby to track down those DNA samples. I want you to escort them to Epsilon Indi."_

Samus was suddenly confused. "If the Federation wanted an escort, they could just assign a security detail. Why would they need me?"

"_A number of reasons."_ Dane held up three finger._ "For one, this isn't a task that can be undertaken using brute force; if the Federation sends its own ships as an escort, they'll be announcing their presence to all hostile forces in the system, and that's just asking for trouble. Second, _you_ have a reputation. If they're smart, they won't come anywhere near your ship. And third…"_ An uncomfortable silence followed as Admiral Dane averted his gaze. _"The CO of this platoon requested your aid personally."_

As the last words left the Admiral's mouth, the hologram projector directly adjacent to him activated. The hologram quickly solidified, taking the form of a man—well-dressed, early- to mid-40's, and the four silver stars of a General adorning his uniform—with a very familiar face.

Adam Malkovich fixed Samus with a steely glare. _"Hello, Samus."_

* * *

**Galactic Federation Archives**

**Relations: Bounty Hunter Samus Aran**

_Samus Aran signed up with the Federation Police at the age of 17. The matter of her age was quietly overlooked in favor of her exemplary testing scores by (then Lieutenant Colonel) Adam Malkovich. There were some in the Federation who criticized Malkovich, noting that Samus had a tendency to defy orders and act on a whim, but these critics were silenced after a reconnaissance mission to the planet Jigrad, where Samus single-handedly shut down a Space Pirate encampment that was using children as slave labor. Samus was shortly thereafter recommended for Officer training; she accepted and spent the next six months working under Malkovich._

_Two weeks following the Malkovich incident on the date of [REDACTED] Samus Aran formally resigned from Officer training and began to take assignments as a Hunter. While relations are mostly highly formal, Samus maintains connections with the Federation and is their most oft-employed Hunter, usually working for no charge. This loss of income is countered by the exorbitant sum of credits required to enlist her services in non-personal assignments, as her mission success rating is an astounding 100%. _

_There is a running joke claiming that one should avoid hiring Samus Aran if an assignment entails work in a military installation, as things have a tendency to self-destruct in her presence._

* * *

We all know how we feel about Other M. It was a horrible excuse for a Metroid game, with bad writing, subpar gameplay (the only really exceptional boss fight was the Vorash lava whale), and underwhelming graphics. Now, an Average Joe like me can't do anything to rectify the latter two, but I CAN do something about the former. This fic is my take on what the Other M storyline SHOULD have been like, and even if it's amateurish, I can guarantee it'll be better than the original.


	2. Meet the Team

Sorry for the long, _long_ wait. Was living my life and such, on top of writing my other story. Be warned—this story won't update very quickly. I'm not as good with writing sci-fi as I am with writing fantasy, but I'll do my best.

An additional note—throughout the many Metroid Games, Samus has had multiple gunships, each designated as Hunter-class. To differentiate between them, I'll refer to the most common gunship, used canonically in Echoes, Metroid II, Super Metroid, and Other M, as the A-Model; and the ship used in Prime 3 (the badass-looking one with all the awesome gadgets) as the B-Model. If you have anything to ask,

XXXXX

"_I see that you two have a history,"_ Admiral Dane grunted. _"I'll leave you to reminisce."_ His hologram abruptly cut out.

Silently cursing Dane for his timing, Samus addressed Adam calmly. "General Malkovich."

"_I've heard quite a bit about your recent achievements. Wiping out the Metroids, killing Mother Brain… you've become an idol of sorts to many people."_

"I only do what I'm paid to," Samus's response was short and simple.

"_Says the Hunter who won't take credit for half the assignments she agrees to."_ Despite the attempt at humor, Adam's face remained cold and expressionless.

An uncomfortable silence followed for the next few seconds. Finally, Samus spoke. "Alright, I'm just going to come out and say it. The two of us didn't exactly part on the best of terms."

"_That, we did not,"_ Adam nodded.

"Which begs the question…" Samus continued. "Why did you seek me out for this mission?"

Adam sighed deeply before answering. _"Call it a gut instinct, but I have a bad feeling about this mission. Whenever you're even remotely involved with something, things tend to spiral out of control. I don't plan on sending innocent men to their deaths if I can help it, so I requested your aid so you can clean up a mess that's at least partially your fault."_

"I never thought you to be the type for superstition, General."

"_If there's anything I've learned after twenty-seven years of working for the Galactic Federation, it's knowing when to trust my gut."_ Adam's gaze bore holes into Samus's forehead as a venomous tone crept into his voice. _"Given your track record, you should know that."_

Samus didn't break eye contact, but if anybody other than Samus was present, they could have seen the slightest twitch of her facial muscles whenever Adam spoke. She nodded. "You have a point, I suppose… Alright, when do we move out?"

"_That's good to hear."_ Adam nodded in return. _"Report to the B-hangar by 1700 hours. The team will be waiting to take off."_

As Adam turned away and the hologram cut off, Samus's tense muscles unclenched. She let out a sigh of frustration and weariness… and promptly flinched as a spike of pain jabbed into her torso. She noticed a drug dispensary nearby.

The temptation started creeping up, but she quickly forced it down. _No, Samus, don't do it. You know what happened the last time you took morphine._

With a groan, she walked out of the medical ward and towards the armory.

XXXXX

"It's a bit more… angular than I remembered." Samus wasn't quite upset, but she _was_ quite confused. The ridges of her shoulder pauldrons were gone, and many of the softly-rounded edges that made up her suit were sharpened.

The Federation engineer nodded. "The alloys that make up your suit aren't exactly alloys the Federation keeps in surplus, Miss Aran. We had to shave off material from undamaged parts of the armor to repair it. It shouldn't hamper performance, though."

Samus stepped forward and flexed her hand. With a flash, the armor collapsed into motes of light and was absorbed by her Zero Suit. "Anything else I should know about?"

"Yes. The damage to your suit's cannon and reactor was extensive; we had to remove a majority of the extension modules." Samus ran a suit diagnostic. After a few seconds, the system report confirmed the engineer's words—her suit had been stripped of missile and energy tanks, although her various upgrades still remained. "However, we've made a breakthrough in manipulating your suit's power distribution."

Samus arched an eyebrow. "How so?"

"We've linked your arm cannon's charging features to your suit's defensive shielding. In an emergency, you can shunt built-up energy in your cannon to restore shields. Additionally, we installed a micro-fabricator as an alternative to scavenging for compatible missiles in the field. The arm cannon will power this, as well."

Old Bird would have blown a fuse if he were around to see his gift to Samus altered like this, but Samus herself was quite pleased. This would cut down on the hours she spent digging through ruins for a resupply.

"Set up a holo-chamber for me, if you would be so kind," Samus said. "I think I'll take this suit for a test-run right now."

XXXXX

Samus stopped at the door and entered her ID code into the keypad. With a soft beep, Samus was granted access to the hangar.

To the left of the bay, Samus spotted a group of soldiers in heavy armor conversing with one another. She walked over to the soldiers of the Galactic Federation 7th Platoon. Noticing Samus entering the chamber, the tallest of the soldiers clapped his hands, grabbing the others' attention, and said in a deep voice, "Soldiers. Stand and present!"

The soldier with the most overall-average body build stood and saluted. "Lyle Smithsonian, Spec Ops," he introduced himself in a gruff, no-nonsense tone.

The next soldier, slightly taller and thinner than the Spec Ops agent, stood and saluted. "Maurice Favreau, engineer and cyberwarfare specialist," he introduced himself with a slight hint of an accent, one Samus just barely identified as something European… possibly Austrian.

The shortest of the group stood and saluted. "K. G. Misawa, advanced reconnaissance," he introduced himself in a quiet voce.

The first soldier to notice her was the last to introduce himself. "Anthony Higgs, heavy weapons."

Something about that last name sparked an old memory in Samus's mind. An old acquaintance, perhaps…? "…Do I know you from somewhere?"

The soldier set his hands on his hips. "Aw, come on, Sammy, don't you remember me?"

A few second's contemplation, and something clicked in her head. "…Tony?"

Higgs threw his hands up. "There you go, Princess!" He flipped open his visor, revealing the dark skin, puffed cheeks, and toothy grin of her old friend. "For a second there, I was worried you'd forgotten me!"

Stepping forward, Samus clasped Higgs's hand and pulled him into a one-armed hug. "Almost did. Thanks for reminding me, Tony."

"Wait, you two know each other?" Smithsonian asked, arms folded. The other two fidgeted nervously; here was this famous, nigh-godlike Hunter standing before them… acting chummy with their second-in-command.

Higgs pointed to himself, then to Samus. "Officer School; boot camp. Bumped into each other in a hallway one day, and we hit it off from there."

Samus saw Favreau arch an eyebrow, and gave him a very cold and stern "Not like _that_."

Higgs laughed. "You gotta forgive the man for assuming, Princess. His mind tends to wander whenever he's off-duty…" For a split-second, his smile grew even wider. "But for the record..." He let the sentence end there, as the others drew their own conclusions.

Everybody started chuckling… save for a certain bounty hunter. Just as Samus cracked her knuckles, preparing to deck the black man over the head in a very _un_-professional display of annoyance, a voice bellowed, "Stand down!" from the doorway.

The smile on each of the soldiers' faces instantly evaporated as they lined up and saluted the newcomer. "Senior officer on deck!" Higgs announced.

General Malkovich eyed each of the soldiers in turn before nodding. "At ease, 7th Platoon."

The soldiers relaxed. "Looks like we'll have time to reminisce later," Higgs's voice echoed in Samus's left ear… as he stood on her right side. She spared a half-amused glance at the man throwing his voice, as did the others.

Malkovich addressed the group calmly. "Alright, men, Samus. Have you been briefed on our mission parameters?"

"Sir, yes sir." All four soldiers and Samus echoed as one.

"Good. So you should all know that in our best-case scenario, we will go in, locate the package, and get out before we're detected. However, I expect you all to be equipped for a full-fledged smash-and-grab assault." To emphasize his point, Adam smacked a fist into his open palm. "I'm talking about Mr. Murphy here, people, so if—or _when_—he snaps his fingers, I want to be absolutely sure that we're prepared for it. Am I clear?"

"Sir, yes sir!"

"Good. We depart at 1710 hours. Dismissed!" At his command, the 7th Platoon moved to pack up their gear into the Federation shuttle docked in the hangar. Meanwhile, Samus was busy tinkering with a datapad.

Adam stepped forward to Samus. "What are you doing?" He asked, gesturing to the datapad.

Samus turned over the datapad. "I just ordered my B-Model Hunter Class gunship to rendezvous with us in Epsilon Indi. If worse comes to worst and we find ourselves in a ship-to-ship dogfight, the B-Model's improved firepower should prove more useful than my A-Model."

Adam glanced at the ship schematics for a moment, and then nodded. "Alright, that's a good plan. Just make sure your gunship stays low; we don't want any unnecessary attention."

Samus nodded. "Rest assured, I won't take any unnecessary risks. Now, I'll be waiting on the ship until we depart."

As she turned to leave, though, Adam's hand gripped her shoulder. "One more thing…"

Samus glanced back. "Yes?"

"Until we know for sure what's waiting for us in Epsilon Indi, I'll have to ask you to power down your suit."

Samus's eyes widened. She turned to face Adam. "Come again?"

"I mean, I want you to deactivate your heavy weapons. You've got armor-piercing plasma weaponry, electromagnetic weaponry, high explosives, and that little mini-nuke you call a power bomb; I do not want to see any of that if it can be helped. I won't ask you to deactivate your suit's other functions—if they help you to operate, I won't stop that."

Samus frowned and folded her arms. "My _weapons_ help me to operate…"

Adam silenced her. "This is about minimizing potential collateral damage and friendly fire. The station we're going is _civilian_-based. That means a token defense force and minimal station hardening. If something happens and you just walk in guns a-blazing, you're going to inflict massive structural damage and put a _lot_ of lives at stake in the process. If that happens, you're going to destroy your own reputation, the reputation of the 7th Platoon, and much, much more. Do you understand me?"

As much as Samus hated to admit it, Adam had a point. Once she was set loose, no matter the objective, she became a one-(wo)man demolition crew—it was in her nature as a warrior. Also in her nature, however, was the drive to protect innocent life. A shootout in a civilian space station would bring both of those sides into conflict with one another and, in doing so, make her a detriment to the mission. On the other hand, doing as Adam requested and purposefully limiting herself would leave her open to a surprise attack—it had happened before. And although Samus had survived regardless of her preparation every time, it was not something Samus enjoyed dealing with.

Finally, Samus decided that restraint was the lesser evil. She sighed and nodded. "So be it. But on one condition: if circumstances call for it, I am allowed to reactivate my weapons."

"That's acceptable, on the grounds that you contact me for authorization, and that such requests will be handled on a case-by-case basis."

"Deal." Samus and Adam quietly shook hands.

Adam checked his PDA. "1708 hours. Alright, Samus, let's get moving."

Samus nodded. Adam turned and boarded the shuttle, the Hunter following close behind. As Samus buckled in, Adam moved up to the cockpit and began the ignition sequence.

At 1710 hours on the dot, the shuttle took off. With a sudden but smooth jerk of motion, the shuttle transitioned to FTL, ferrying its passengers to a new adventure.


End file.
